R Notebook

library(tidyverse)
library(Biostrings)
library(DECIPHER)
library(ggseqlogo)
library(htmltools)
library(plotly)

petases <- readAAStringSet("seqdump.txt")
petases <- AAStringSet(petases)
aligned_petases <- AlignSeqs(petases)

## Determining distance matrix based on shared 5-mers:
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## Time difference of 0 secs
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## Clustering into groups by similarity:
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## Time difference of 0.06 secs
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## Aligning Sequences:
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## Time difference of 0.12 secs
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## Iteration 1 of 2:
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## Determining distance matrix based on alignment:
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## Time difference of 0 secs
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## Reclustering into groups by similarity:
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## Time difference of 0 secs
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## Realigning Sequences:
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## Time difference of 0.11 secs
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## Iteration 2 of 2:
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## Determining distance matrix based on alignment:
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## Time difference of 0 secs
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## Reclustering into groups by similarity:
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## Time difference of 0 secs
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## Realigning Sequences:
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## Time difference of 0.01 secs

BrowseSeqs(aligned_petases, htmlFile = "output.html", openURL = FALSE)
htmltools::includeHTML("output.html")

                                                                                                       20                  40                  60                  80                 100                 120                 140                 160                 180                 200                 220                 240                 260                 280                 300        
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    6ILX_A Chain A, Poly(ethylene terephthalate) hydrolase [Ideonella sakaiensis]    --------------------------MQTNPYARGPNPTAASLEASAGPFTVRSFTVSRPSGYGAGTVYYPTNAGGTVGAIAIVPGYTARQSSIKWWGPRLASHGFVVITIDTNSTLDQPSSRSSQQMAALRQVASLNGTSSSPIYGKVDTARMGVMGFSMGGGGSLISAANNPSLKAAAPQAPWDSSTNFSSVTVPTLIFACENDSIAPVNSSALPIYDSMSRNAKQFLEINGGSHSCANSGNSNQALIGKKGVAWMKRFMDNDTRYSTFACENPNSTRVSDFRTANCS--HHHHHH--------------    270    
    5XFY_A Chain A, Poly(ethylene terephthalate) hydrolase [Ideonella sakaiensis]    -----------------------------NPYARGPNPTAASLEASAGPFTVRSFTVSRPSGYGAGTVYYPTNAGGTVGAIAIVPGYTARQSSIKWWGPRLASHGFVVITIDTNSTLDQPSSRSSQQMAALRQVASLNGTSSSPIYGKVDTARMGVMGWAMGGGGSLISAANNPSLKAAAPQAPWDSSTNFSSVTVPTLIFACENDSIAPVNSSALPIYDSMSRNAKQFLEINGGSHSCANSGNSNQALIGKKGVAWMKRFMDNDTRYSTFACENPNSTRVSDFRTANCS----------------------    261    
    5XJH_A Chain A, Poly(ethylene terephthalate) hydrolase [Ideonella sakaiensis]    ------------MGSSHHHHHHSSGLVPRGSHMRGPNPTAASLEASAGPFTVRSFTVSRPSGYGAGTVYYPTNAGGTVGAIAIVPGYTARQSSIKWWGPRLASHGFVVITIDTNSTLDQPSSRSSQQMAALRQVASLNGTSSSPIYGKVDTARMGVMGWSMGGGGSLISAANNPSLKAAAPQAPWDSSTNFSSVTVPTLIFACENDSIAPVNSSALPIYDSMSRNAKQFLEINGGSHSCANSGNSNQALIGKKGVAWMKRFMDNDTRYSTFACENPNSTRVSDFRTANCSLEDPAANKARKEAELAAATAEQ    300    
    5XFZ_A Chain A, Poly(ethylene terephthalate) hydrolase [Ideonella sakaiensis]    ----------------------------MNPYARGPNPTAASLEASAGPFTVRSFTVSRPSGYGAGTVYYPTNAGGTVGAIAIVPGYTARQSSIKWWGPRLASHGFVVITIDTNSTLDQPSSRSSQQMAALGQVASLNGTSSSPIYGKVDTARMGVMGWAMGGGGSLISAANNPSLKAAAPQAPWDSSTNFSSVTVPTLIFACENDSIAPVNSSALPIYDSMSRNAKQFLEINGGSHSCANSGNSNQALIGKKGVAWMKRFMDNDTRYSTFACENPNSTRVSDFRTANCS----------------------    262    
    5XH3_A Chain A, Poly(ethylene terephthalate) hydrolase [Ideonella sakaiensis]    -----------------------------NPYARGPNPTAASLEASAGPFTVRSFTVSRPSGYGAGTVYYPTNAGGTVGAIAIVPGYTARQSSIKWWGPRLASHGFVVITIDTNSTLDQPSSRSSQQMAALGQVASLNGTSSSPIYGKVDTARMGVMGWAMGGGGSLISAANNPSLKAAAPQAPWDSSTNFSSVTVPTLIFACENDSIAPVNSSALPIYDSMSRNAKQFLEINGGSHSCANSGNSNQALIGKKGVAWMKRFMDNDTRYSTFACENPNSTRVSDFRTANCS----------------------    261    
    6KUO_A Chain A, Poly(ethylene terephthalate) hydrolase [Ideonella sakaiensis]    ------------MGSSHHHHHHSSGLVPRGSHMRGPNPTAASLEASAGPFTVRSFTVSRPSGYGAGTVYYPTNAGGTVGAIAIVPGYTARQSSIKWWGPRLASHGFVVITIDTNSTLDQPSSRSSQQMAALRQVASLNGTSSSPIYGKVDTARMGVMGWSMGGGGSLISAANNPSLKAAAPQAPWDSSTNFSSVTVPTLIFACENDSIAPVNSSALPIYDSMSRNAKQFLEINGGSHSCANSGNSDQALIGKKGVAWMKRFMDNDTRYSTFACENPNSTRVSDFRTANCSLEDPAANKARKEAELAAATAEQ    300    
    5YNS_A Chain A, Poly(ethylene terephthalate) hydrolase [Ideonella sakaiensis]    -----------------------------GSHMRGPNPTAASLEASAGPFTVRSFTVSRPSGYGAGTVYYPTNAGGTVGAIAIVPGYTARQSSIKWWGPRLASHGFVVITIDTNSTLDQPSSRSSQQMAALRQVASLNGTSSSPIYGKVDTARMGVMGWSMGGGGSLISAANNPSLKAAAPQAPWDSSTNFSSVTVPTLIFACENDSIAPVNSSALPIYDSMSRNAKQFLEINGGSHSCANSGNSNQALIGKKGVAWMKRFMDNDTRYSTFACENPNSTAVSDFRTANCSLED-------------------    264    
    6IJ5_A Chain A, Poly(ethylene terephthalate) hydrolase [Ideonella sakaiensis]    ------------MGSSHHHHHHSSGLVPRGSHMRGPNPTAASLEASAGPFTVRSFTVSRPSGYGAGTVYYPTNAGGTVGAIAIVPGYTARQSSIKWWGPRLASHGFVVITIDTNSTLDQPSSRSSQQMAALRQVASLNGTSSSPIYGKVDTARMGVMGWSMGGGGSLISAANNPSLKAAAAQAPWDSSTNFSSVTVPTLIFACENDSIAPVNSSALPIYDSMSRNAKQFLEINGGSHSCANSGNSNQALIGKKGVAWMKRFMDNDTRYSTFACENPNSTRVSDFRTANCSLEDPAANKARKEARLAAATAEQ    300    
    5YFE_A Chain A, Poly(ethylene terephthalate) hydrolase [Ideonella sakaiensis]    --------------------------AQTNPYARGPNPTAASLEASAGPFTVRSFTVSRPSGYGAGTVYYPNNAGGTVGAIAIVPGYTARQSSIKWWGPRLASHGFVVITIDTNSTLDQPSSRSSQQMAALRQVASLNGTSSSPIYGKVDTARMGVMGWSMGGGGSLISAANNPSLKAAAPQAPWDSSTNFSSVTVPTLIFACENDSIAPVNSSALPIYDSMSANAKQFLEINGGSHSCANSGNSNQALIGKKGVAWMKRFMDNDTRYSTFACENPNSTRVSDFRTNNCSLEHHHHHH--------------    272    
    6IJ4_A Chain A, Poly(ethylene terephthalate) hydrolase [Ideonella sakaiensis]    ------------MGSSHHHHHHSSGLVPRGSHMRGPNPTAASLEASAGPFTVRSFTVSRPSGYGAGTVYYPTNAGGTVGAIAIVPGYTARQSSIKWWGPRLASHGFVVITIDTNSTLDQPESRSSQQMAALRQVASLNGTSSSPIYGKVDTARMGVMGWSMGGGGSLISAANNPSLKAAAPQAPWHSSTNFSSVTVPTLIFACENDSIAPVNSSALPIYDSMSRNAKQFLEINGGSHSCANSGNSNQALIGKKGVAWMKRFMDNDTRYSTFACENPNSTRVSDFRTANCSLEDPAANKARKEARLAAATAEQ    300    
    6KUQ_A Chain A, Poly(ethylene terephthalate) hydrolase [Ideonella sakaiensis]    ------------MGSSHHHHHHSSGLVPRGSHMRGPNPTAASLEASAGPFTVRSFTVSRPSGYGAGTVYYPTNAGGTVGAIAIVPGYTARQSSIKWWGPRLASHGFVVITIDTNSTLDQPSSRSSQQMAALRQVASLNGTSSSPIYGKVDTARMGVMGWSMGGGGSLISAANNPSLKAAAPQAPWDSSTNFSSVTVPTLIFACENDSIAPVNSSALPIYDSMSRNAKQFLEINGGSHSCANSGNSNQDLIGKKGVAWMKRFMDNDTRYSTFACENPNSTKVSDFRTANCSLEDPAANKARKEAELAAATAEQ    300    
    6IJ3_A Chain A, Poly(ethylene terephthalate) hydrolase [Ideonella sakaiensis]    ------------MGSSHHHHHHSSGLVPRGSHMRGPNPTAASLEASAGPFTVRSFTVSRPSGYGAGTVYYPTNAGGTVGAIAIVPGYTARQSSIKWWGPRLASHGFVVITIDTNSTLDQPDSRSSQQMAALRQVASLNGTSSSPIYGKVDTARMGVMGWSMGGGGSLISAANNPSLKAAAPQAPWHSSTNFSSVTVPTLIFACENDSIAPVNSSALPIYDSMSRNAKQFLEINGGSHSCANSGNSNQALIGKKGVAWMKRFMDNDTRYSTFACENPNSTRVSDFRTANCSLEDPAANKARKEARLAAATAEQ    300    
    6IJ6_A Chain A, Poly(ethylene terephthalate) hydrolase [Ideonella sakaiensis]    ------------MGSSHHHHHHSSGLVPRGSHMRGPNPTAASLEASAGPFTVRSFTVSRPSGYGAGTVYYPTNAGGTVGAIAIVPGYTARQSSIKWWGPRLASHGFVVITIDTNSTLDQPESRSSQQMAALRQVASLNGTSSSPIYGKVDTARMGVMGWSMGGGGSLISAANNPSLKAAAPQAPWHSSTNFSSVTVPTLIFACENDSIAPVNSSALPIYDSMSRNAKQFLEINGGSHSCANSGNSNQALIGKKGVAWMKRFMDNDTRYSTFACENPNSTAVSDFRTANCSLEDPAANKARKEARLAAATAEQ    300    
    6KUS_A Chain A, Poly(ethylene terephthalate) hydrolase [Ideonella sakaiensis]    ------------MGSSHHHHHHSSGLVPRGSHMRGPNPTAASLEASAGPFTVRSFTVSRPSGYGAGTVYYPTNAGGTVGAIAIVPGYTARQSSIKWWGPRLASHGFVVITIDTNSTLDQPESRSSQQMAALRQVASLNGTSSSPIYGKVDTARMGVMGWSMGGGGSLISAANNPSLKAAAPQAPWHSSTNFSSVTVPTLIFACENDSIAPVNSSALPIYDSMSRNAKQFLEINGGSHSCANTGNSDQALIGKKGVAWMKRFMDNDTRYSTFACENPNSTRVSDFRTANCSLEDPAANKARKEAELAAATAEQ    300    
                             6KY5_A Chain A, PET hydrolase [Ideonella sakaiensis]    MNFPRASRLMQAAVLGGLMAVSAAATAQTNPYARGPNPTAASLEASAGPFTVRSFTVSRPSGYGAGTVYYPTNAGGTVGAIAIVPGYTARQSSIKWWGPRLASHGFVVITIDTNSTFDYPSSRSSQQMAALRQVASLNGDSSSPIYGKVDTARMGVMGHSMGGGASLRSAANNPSLKAAIPQAPWDSQTNFSSVTVPTLIFACENDSIAPVNSHALPIYDSMSRNAKQFLEINGGSHSCANSGNSNQALIGKKGVAWMKRFMDNDTRYSTFACENPNSTAVSDFRTANCSLEHHHHHH--------------    298    
                                                                                             
                                                                        Consensus    MNFPRASRLMQAXXXXXXXXXXXXXXXXXXXXXRGPNPTAASLEASAGPFTVRSFTVSRPSGYGAGTVYYPXNAGGTVGAIAIVPGYTARQSSIKWWGPRLASHGFVVITIDTNSTXDXPXSRSSQQMAALXQVASLNGXSSSPIYGKVDTARMGVMGXXMGGGXSLXSAANNPSLKAAXXQAPWXSXTNFSSVTVPTLIFACENDSIAPVNSXALPIYDSMSXNAKQFLEINGGSHSCANXGNSBQXLIGKKGVAWMKRFMDNDTRYSTFACENPNSTXVSDFRTXNCS++XXXXXXARKEAXLAAATAEQ    312    
                                                                                             
                                                                                             

ggplotly(ggseqlogo(as.character(aligned_petases)), width = 5000)

## Warning: `group_by_()` is deprecated as of dplyr 0.7.0.
## Please use `group_by()` instead.
## See vignette('programming') for more help
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_warnings()` to see where this warning was generated.